data_UPE # _chem_comp.id UPE _chem_comp.name ;2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C18 H22 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-11-07 _chem_comp.pdbx_modified_date 2012-11-16 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 455.356 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UPE _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4HQU _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal UPE P P P 0 1 N N N 2.319 -3.351 12.059 -6.729 1.974 -0.098 P UPE 1 UPE N1 N1 N 0 1 N N N 7.501 -5.274 9.853 -0.736 -1.078 0.044 N1 UPE 2 UPE C2 C2 C 0 1 N N N 8.729 -5.482 9.181 -0.856 -1.031 1.380 C2 UPE 3 UPE O2 O2 O 0 1 N N N 8.758 -5.510 7.938 -1.955 -1.184 1.877 O2 UPE 4 UPE N3 N3 N 0 1 N N N 9.882 -5.659 9.843 0.198 -0.820 2.186 N3 UPE 5 UPE C4 C4 C 0 1 N N N 9.918 -5.646 11.179 1.432 -0.647 1.666 C4 UPE 6 UPE O4 O4 O 0 1 N N N 11.009 -5.810 11.763 2.391 -0.456 2.391 O4 UPE 7 UPE C5 C5 C 0 1 N N N 8.647 -5.424 11.923 1.592 -0.694 0.204 C5 UPE 8 UPE C6 C6 C 0 1 N N N 7.479 -5.248 11.187 0.467 -0.914 -0.566 C6 UPE 9 UPE "C1'" "C1'" C 0 1 N N R 6.244 -5.068 9.118 -1.927 -1.317 -0.774 "C1'" UPE 10 UPE "C2'" "C2'" C 0 1 N N N 5.686 -6.337 8.490 -2.541 -2.695 -0.440 "C2'" UPE 11 UPE C21 C21 C 0 1 N N N 8.539 -5.363 13.423 2.911 -0.512 -0.419 C21 UPE 12 UPE O22 O22 O 0 1 N N N 7.412 -5.212 13.898 3.042 -0.656 -1.620 O22 UPE 13 UPE N23 N23 N 0 1 N N N 9.609 -5.436 14.222 3.976 -0.185 0.340 N23 UPE 14 UPE C24 C24 C 0 1 N N N 9.450 -5.354 15.675 5.265 0.106 -0.292 C24 UPE 15 UPE C25 C25 C 0 1 N N N 10.612 -6.081 16.327 6.297 0.445 0.786 C25 UPE 16 UPE C26 C26 C 0 1 Y N N 10.468 -7.580 16.365 7.623 0.744 0.136 C26 UPE 17 UPE C27 C27 C 0 1 Y N N 11.609 -8.335 16.683 7.932 2.038 -0.241 C27 UPE 18 UPE C28 C28 C 0 1 Y N N 11.549 -9.727 16.722 9.148 2.312 -0.837 C28 UPE 19 UPE C29 C29 C 0 1 Y N N 10.337 -10.357 16.446 10.056 1.293 -1.057 C29 UPE 20 UPE "C3'" "C3'" C 0 1 N N S 4.188 -6.135 8.505 -4.065 -2.458 -0.528 "C3'" UPE 21 UPE "O3'" "O3'" O 0 1 N N N 3.805 -5.607 7.234 -4.642 -3.282 -1.544 "O3'" UPE 22 UPE C30 C30 C 0 1 Y N N 9.204 -9.597 16.120 9.747 -0.001 -0.681 C30 UPE 23 UPE C31 C31 C 0 1 Y N N 9.259 -8.203 16.086 8.532 -0.274 -0.079 C31 UPE 24 UPE "C4'" "C4'" C 0 1 N N R 3.933 -5.048 9.534 -4.192 -0.966 -0.905 "C4'" UPE 25 UPE "O4'" "O4'" O 0 1 N N N 5.221 -4.605 9.998 -2.962 -0.364 -0.447 "O4'" UPE 26 UPE "C5'" "C5'" C 0 1 N N N 3.022 -5.512 10.672 -5.390 -0.336 -0.191 "C5'" UPE 27 UPE "O5'" "O5'" O 0 1 N N N 3.203 -4.682 11.818 -5.560 1.009 -0.640 "O5'" UPE 28 UPE OP1 OP1 O 0 1 N N N 1.279 -3.231 10.965 -8.041 1.317 -0.291 OP1 UPE 29 UPE OP2 OP2 O 0 1 N N N 1.850 -3.306 13.495 -6.500 2.266 1.469 OP2 UPE 30 UPE OP3 OP3 O 0 1 N Y N 3.349 -2.163 11.868 -6.699 3.363 -0.912 OP3 UPE 31 UPE HN3 HN3 H 0 1 N N N 10.728 -5.803 9.329 0.072 -0.792 3.147 HN3 UPE 32 UPE H6 H6 H 0 1 N N N 6.543 -5.088 11.702 0.542 -0.956 -1.643 H6 UPE 33 UPE "H1'" "H1'" H 0 1 N N N 6.410 -4.329 8.320 -1.677 -1.258 -1.833 "H1'" UPE 34 UPE "H2'" "H2'" H 0 1 N N N 6.053 -6.455 7.460 -2.227 -3.440 -1.172 "H2'" UPE 35 UPE "H2'A" "H2'A" H 0 0 N N N 5.966 -7.220 9.083 -2.260 -3.005 0.566 "H2'A" UPE 36 UPE HN23 HN23 H 0 0 N N N 10.520 -5.547 13.826 3.888 -0.143 1.306 HN23 UPE 37 UPE H24 H24 H 0 1 N N N 9.448 -4.300 15.989 5.600 -0.767 -0.853 H24 UPE 38 UPE H24A H24A H 0 0 N N N 8.502 -5.827 15.972 5.155 0.953 -0.969 H24A UPE 39 UPE H25 H25 H 0 1 N N N 11.527 -5.838 15.767 5.962 1.318 1.347 H25 UPE 40 UPE H25A H25A H 0 0 N N N 10.707 -5.719 17.361 6.407 -0.402 1.463 H25A UPE 41 UPE H27 H27 H 0 1 N N N 12.540 -7.833 16.899 7.223 2.834 -0.069 H27 UPE 42 UPE H28 H28 H 0 1 N N N 12.427 -10.308 16.962 9.390 3.323 -1.131 H28 UPE 43 UPE H29 H29 H 0 1 N N N 10.270 -11.434 16.483 11.006 1.507 -1.524 H29 UPE 44 UPE "H3'" "H3'" H 0 1 N N N 3.657 -7.064 8.760 -4.538 -2.651 0.435 "H3'" UPE 45 UPE "HO3'" "HO3'" H 0 0 N N N 2.865 -5.471 7.217 -4.537 -4.230 -1.388 "HO3'" UPE 46 UPE H30 H30 H 0 1 N N N 8.275 -10.098 15.892 10.455 -0.798 -0.854 H30 UPE 47 UPE H31 H31 H 0 1 N N N 8.381 -7.622 15.848 8.293 -1.284 0.219 H31 UPE 48 UPE "H4'" "H4'" H 0 1 N N N 3.432 -4.212 9.024 -4.291 -0.854 -1.984 "H4'" UPE 49 UPE "H5'" "H5'" H 0 1 N N N 1.974 -5.455 10.344 -6.289 -0.911 -0.415 "H5'" UPE 50 UPE "H5'A" "H5'A" H 0 0 N N N 3.268 -6.552 10.934 -5.215 -0.341 0.885 "H5'A" UPE 51 UPE HOP2 HOP2 H 0 0 N N N 0.906 -3.202 13.517 -5.658 2.697 1.670 HOP2 UPE 52 UPE HOP3 HOP3 H 0 0 N Y N 3.094 -1.639 11.118 -7.378 3.995 -0.637 HOP3 UPE 53 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal UPE OP1 P DOUB N N 1 UPE "O5'" P SING N N 2 UPE OP3 P SING N N 3 UPE P OP2 SING N N 4 UPE "C1'" N1 SING N N 5 UPE C2 N1 SING N N 6 UPE N1 C6 SING N N 7 UPE O2 C2 DOUB N N 8 UPE C2 N3 SING N N 9 UPE N3 C4 SING N N 10 UPE N3 HN3 SING N N 11 UPE C4 O4 DOUB N N 12 UPE C4 C5 SING N N 13 UPE C6 C5 DOUB N N 14 UPE C5 C21 SING N N 15 UPE C6 H6 SING N N 16 UPE "C2'" "C1'" SING N N 17 UPE "C1'" "O4'" SING N N 18 UPE "C1'" "H1'" SING N N 19 UPE "C2'" "C3'" SING N N 20 UPE "C2'" "H2'" SING N N 21 UPE "C2'" "H2'A" SING N N 22 UPE C21 O22 DOUB N N 23 UPE C21 N23 SING N N 24 UPE N23 C24 SING N N 25 UPE N23 HN23 SING N N 26 UPE C24 C25 SING N N 27 UPE C24 H24 SING N N 28 UPE C24 H24A SING N N 29 UPE C25 C26 SING N N 30 UPE C25 H25 SING N N 31 UPE C25 H25A SING N N 32 UPE C31 C26 DOUB Y N 33 UPE C26 C27 SING Y N 34 UPE C27 C28 DOUB Y N 35 UPE C27 H27 SING N N 36 UPE C29 C28 SING Y N 37 UPE C28 H28 SING N N 38 UPE C30 C29 DOUB Y N 39 UPE C29 H29 SING N N 40 UPE "O3'" "C3'" SING N N 41 UPE "C3'" "C4'" SING N N 42 UPE "C3'" "H3'" SING N N 43 UPE "O3'" "HO3'" SING N N 44 UPE C31 C30 SING Y N 45 UPE C30 H30 SING N N 46 UPE C31 H31 SING N N 47 UPE "C4'" "O4'" SING N N 48 UPE "C4'" "C5'" SING N N 49 UPE "C4'" "H4'" SING N N 50 UPE "C5'" "O5'" SING N N 51 UPE "C5'" "H5'" SING N N 52 UPE "C5'" "H5'A" SING N N 53 UPE OP2 HOP2 SING N N 54 UPE OP3 HOP3 SING N N 55 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor UPE SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(N2C(=O)NC(=O)C(C(=O)NCCc1ccccc1)=C2)CC3O" UPE InChI InChI 1.03 "InChI=1S/C18H22N3O9P/c22-13-8-15(30-14(13)10-29-31(26,27)28)21-9-12(17(24)20-18(21)25)16(23)19-7-6-11-4-2-1-3-5-11/h1-5,9,13-15,22H,6-8,10H2,(H,19,23)(H,20,24,25)(H2,26,27,28)/t13-,14+,15+/m0/s1" UPE InChIKey InChI 1.03 CBTXGTWTWUZPNV-RRFJBIMHSA-N UPE SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCCc3ccccc3)C(=O)NC2=O" UPE SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCCc3ccccc3)C(=O)NC2=O" UPE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CCNC(=O)C2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" UPE SMILES "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CCNC(=O)C2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(O)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier UPE "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate) ; UPE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-5-(2-phenylethylcarbamoyl)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UPE "Create component" 2012-11-07 RCSB UPE "Initial release" 2012-11-16 RCSB #